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HotKnots specifications


Unique identifier OMICS_03456
Name HotKnots
Interface Web user interface
Restrictions to use None
Programming languages C, C++
Computer skills Basic
Stability Stable
Maintained Yes

Publication for HotKnots

HotKnots in publications

PMCID: 4109605
PMID: 25110687
DOI: 10.1155/2014/690340

[…] folding by dynamically folding rna structures according to the above golden section points. the sensitivity and number of predicted pseudoknots of our algorithm are better than those of the mfold, hotknots, mcqfold, probknot, and lhw-zhu algorithms. experimental results reflect the folding rules of rna from a new angle that is close to natural folding., rnas are versatile molecules. messenger […]

PMCID: 3952952
PMID: 24564983
DOI: 10.1186/1472-6807-13-S1-S3

[…] only for non-pseudoknotted sequences are unafold (2008) and rnafold (1994). the programs that predict both pseudoknotted and non-pseudoknotted sequences are ipknot (2011), pknotsrg (2007), hotknots (2005), nupack (2004), and pknots(1998). these prediction programs, which typically involve some form of minimization of free energy, maximization of expected accuracy, or dynamic […]

PMCID: 3337422
PMID: 22558001
DOI: 10.3389/fgene.2012.00036

[…] we have previously proposed for pseudoknot-free rna inverse folding. in the new version of modena, (i) a new crossover operator is implemented and (ii) pseudoknot prediction methods, ipknot and hotknots, are used to evaluate the designed rna sequences, allowing us to perform the inverse folding of pseudoknotted rnas. the new version of modena with the new crossover operator was benchmarked […]

PMCID: 3177178
PMID: 21653559
DOI: 10.1093/nar/gkr305

[…] state, rather than any of the partially folded intermediates, we therefore attribute it to an off-pathway, ‘misfolded’ structure. figure 4., a search of suboptimal structures using mfold () and hotknots () revealed two possible candidates for state m: a potential pseudoknot involving 29 nts that would normally form hairpin p2 and the 5′-end of p1, or a hairpin made from 32 nts which would […]

PMCID: 1802631
PMID: 17179177
DOI: 10.1093/nar/gkl943

[…] between two partner sequences. combined with the mfold, plmm_dpss can also be used in predicting complicated pseudoknots. the test results of plmm_dpss, pknots, iterated loop matching, pknotsrg and hotknots with pseudobase sequences have shown that plmm_dpss is the most sensitive among the five methods. plmm_dpss also provides manageable pseudoknot folding scenarios for further structure […]

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HotKnots institution(s)
Department of Computer Science, University of British Columbia, Vancouver, BC, Canada

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